TB-Profiler result

Run: SRR25827327

Summary

Run ID: SRR25827327

Sample name:

Date: 01-02-2024 00:33:17

Number of reads: 3834188

Percentage reads mapped: 49.88

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (0.96)
Isoniazid R katG p.Ser315Thr (0.89)
Ethambutol R embA c.-16C>T (0.59)
Pyrazinamide R pncA c.-11A>G (0.91)
Streptomycin R rpsL p.Lys43Arg (0.86)
Fluoroquinolones R gyrA p.Ala90Val (0.82)
Moxifloxacin R gyrA p.Ala90Val (0.82)
Ofloxacin R gyrA p.Ala90Val (0.82)
Levofloxacin R gyrA p.Ala90Val (0.82)
Ciprofloxacin R gyrA p.Ala90Val (0.82)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 0.95
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.96
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.96
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
gyrA 7570 p.Ala90Val missense_variant 0.82 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.96 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.86 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.89 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 0.91 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.59 ethambutol
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 0.9
fgd1 491742 c.960T>C synonymous_variant 0.97
mshA 575907 p.Ala187Val missense_variant 0.96
ccsA 620625 p.Ile245Met missense_variant 0.92
rpoC 763031 c.-339T>C upstream_gene_variant 0.97
rpoC 764666 p.Gly433Ser missense_variant 0.9
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 776182 p.Asp767Asn missense_variant 0.97
mmpS5 779615 c.-710C>G upstream_gene_variant 0.98
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 0.97
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.94
PPE35 2167926 p.Leu896Ser missense_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568425 c.255T>G synonymous_variant 0.19
whiB7 3568428 c.252A>C synonymous_variant 0.24
Rv3236c 3612813 p.Thr102Ala missense_variant 0.95
embC 4241022 p.Ala387Val missense_variant 0.85
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.96
embB 4247729 p.Gly406Thr missense_variant 0.59
aftB 4267647 p.Asp397Gly missense_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.93
gid 4407620 p.Tyr195His missense_variant 0.86
gid 4407927 p.Glu92Asp missense_variant 0.96